EDIT:

I edited my latex file and removed\usepackage{hyperref}. This definitely got rid of the ! LaTeX Error: Option clash for package hyperref. message but now the arXiv TeX compiler gives me a fatal error after several package natbib warnings for all the references.

Them start with commenting on package, compile. Error? Next commented package. Error? until you find the package that causes the clash. Then rearange your packages. hyperref should be the last, see the documetation of hyperref for more informations ...
–
KurtJun 11 '13 at 15:25

1 Answer
1

I had to contact the folks at arXiv and they asked me to include authblk.sty
setspace.sty, subfig.sty, caption.sty, caption2.sty, caption3.sty, babel.sty with my .tex document and eps figures and .bbl file.

Apparently these style files are the only packages that might be mixed versions from what we're running in our environment.